Genetics
experts
at the
Smithsonian’s
National Zoo
crack codes
to solve
animal
mysteries

by Susan Lumpkin

If there are mysteries to
be solved at the National
Zoo, genetics expert Robert
Fleischer and his team in the
Zoo’s Genetics Lab are often
called to action. After a prehensile-
tailed porcupine was born last summer,
there was no easy way to determine its sex.
All it took was one quill from the porcupine
kit, and the lab scientists were able to
conduct a DNA analysis to determine that
the fluffy youngster was a female. The same
process answered Zoo keepers’ questions
about a newly hatched kiwi—just one
feather was enough to say, “It’s a boy!”
The Genetics Lab also conducts paternity
analyses to verify “who’s the father” of
some Zoo babies. Other times, the scientists
help the Zoo’s pathologists by checking
for deadly chytrid fungus in frogs and
for other parasites in birds and mammals.

When a Zoo crane died in 2008, a bite
wound suggested it was killed by a carnivore
that sneaked into its enclosure, a highly unusual event, even given that the Zoo is
set within a natural area full of wild predatory
animals. But which of the potential
suspects that roam Rock Creek Park was
it? A feral dog or cat, a coyote, or one of
two kinds of fox that inhabit the park? To
solve the mystery, Fleischer went into “CSI
mode,” referring to the popular crime-solving
television drama. He and his colleagues
managed to collect saliva from the bite and
use sophisticated equipment to analyze the
DNA in the saliva. They were then able to
match the DNA code in the saliva to the
known DNA of a particular species. The
genetic clues left no doubt: It was a gray fox
that did the deed. This knowledge enabled
keepers to appropriately bolster the defenses
of bird enclosures, successfully preventing
any further such incident.

“DNA is DNA,” says Fleischer. That’s
why his lab can handle samples from
such a diverse array of species to answer a
questions about mammals that range from bats to elephants, birds from sparrows to
ostriches, and a wide range of other organisms
including fish, mosquitoes, protozoan
parasites, and bacteria. Some of the studies
conducted in the lab are part of long-term
research projects by lab scientists and their
close colleagues in the Zoo’s other science
centers and at the Smithsonian’s National
Museum of Natural History (NMNH).
Others are carried out by graduate and
postdoctoral students who come to the
lab as one of the few place to do the DNA
analyses required to answer their research
questions.

Bigger, Faster, Drier

A feather from a newly-hatched kiwi
chick contained information about its gender
and more. (Jessie Cohen/NZP)

All of this state-of-the-art sleuthing has
been done inside an unassuming old stone
building right on the Zoo’s grounds. The
Genetics Lab, founded by Fleischer in
1991, is a section of the Zoo’s Center for
Conservation and Evolutionary Genetics,
which Fleischer now heads. The lab has
an unusual Smithsonian history. It was
first part of the Zoo, then became part of
NMNH, and is now a joint program of
both—all without ever moving an inch
from its original quarters in the old Propagation
Building behind the Small Mammal
House. The Prop Building is not only old
and cramped, it’s prone to flooding whenever
Rock Creek’s waters spill over.

Soon the lab can weather rainstorms
with no problem. In October, the 15 or so
scientists and students currently working
at the Genetics Lab will move their base
of operations from the Prop Building to
a sparkling new lab space set on higher
ground at the Zoo. The new Genetics Lab
will offer bench space for 15 people to work
without doubling up and a more efficient
layout. Better yet, the new lab’s location—near the vet hospital, the Conservation
and Science building, and the pathology
department—will facilitate the staff’s
collaboration with those units. And for
Fleischer and his colleague Jesus Maldonado,
collaboration is the name of the game
in applying genetic analysis to solve new
problems, whether it is within the Zoo,
with their Smithsonian colleagues, or with
scientists around the world.

Secrets From the Past

They say dead men tell no tales, but today
even extinct species can talk to us. They
speak in the language of their DNA, translated
by scientists through sophisticated
processes that make their stories intelligible.
Fleischer, Maldonado, and other scientists
who work in the Genetics Lab are among
the world’s best translators. They are detectives
who decipher the language of genes
to solve a host of biological mysteries about
extinct species and living ones, too. They
investigate cold cases, such as tracing the
evolutionary history of an extinct, mostly
stripeless zebra known as a quagga. They
pursue hot cases, such as predicting the
global spread of bird flu.

A specialty of the Genetics Lab is studying
ancient DNA, and the lab is one of
only a handful in North America with recognized
excellence in the tricky procedures
necessary to get reliable results. Ancient
DNA is extracted from a no-longer-living
source, such as hair, tissue, or teeth from
museum specimens or bones preserved
naturally in permafrost. Sometimes the
sample is recent, and other times it dates to
hundreds of thousands of years ago.

Hidden Meaning

Beyond solving mysteries of the past,
genetic studies have very real applications
to our world today. Very often research
using ancient, modern, or both types of
DNA can help scientists better conserve
living species.

Working with colleagues from the
Wildlife Institute of India, and using both
modern and ancient DNA, Maldonado
and Fleischer discovered that the Indian
subcontinent was home to two distinct
ancient lineages of wolf: an Indian wolf
and a Himalayan wolf. These wolves were
previously lumped with the wide-ranging
gray wolf species that we know in North
America and Eurasia. Finding out that
they are probably two different species is extremely important from the conservation
planning point of view. The Indian wolf
population consists of only 2,000 to 3,000
animals, while the Himalayan wolf in
India may number as few as 350 individuals.
Little is known about either of these
wolves, but both are persecuted by people
and are not legally protected. Knowing
that the Indian and Himalayan wolves are
in greater danger of extinction than the
better-known gray wolves helps conservationists
target their efforts.

Another leadership area of the Genetics
Lab is using non-invasive methods to
collect DNA from living animals—many
of which are hard to find or observe, much
less catch. What clues can scientists use
that animals leave behind? Answers can
often be found in their poop. Maldonado
and others have been perfecting methods
to extract and study DNA from feces.
This yields valuable information about an
animal’s ecology, behavior, and genetics—and the more you know, the easier it is to
help it.

In a research project on endangered San
Joaquin kit foxes in California, Maldonado,
Katherine Ralls, a research scientist in the
Center for Conservation and Evolutionary
Genetics, and others systematically collected
the foxes’ scat with the help of specially
trained dogs. Once they extracted DNA
from the kit fox scat, they were able to
identify individuals and their sex, to track
the foxes’ movements through the study
site, and even to understand social relationships
by counting the number of individual
foxes that contributed their scat to shared
latrines and measuring their kinship.

Maned wolves offer valuable
clues to geneticists.(Mehgan Murphy/NZP)

Similarly, Maldonado is working with
Louise Emmons of NMNH to apply scat
DNA analysis in her study of maned wolves
in Argentina. Looking at samples from
Argentinean maned wolves as well as those
from wolves in the Zoo’s breeding colony at the Front Royal, Virginia, campus—which originated from Brazil—they learned that
maned wolves as a species have low genetic
diversity. Fortunately for their conservation
in Argentina, the animals in Emmons’
study site exhibit a good amount of the
genetic variability that exists in the species.
The scientists are also using scat DNA to
determine kinship among individuals in
her study area to determine, for instance,
whether neighbors are closely related in
order to better understand the population’s
social structure.

In a new collaboration with the Zoo’s
Conservation Ecology Center, analysis
of DNA extracted from tiger scats will
be used to determine how much, if any,
genetic interchange exists between tiger
populations living in different Indian tiger
reserves. Maldonado is also working with
Penny Spiering of the Zoo’s Center for
Species Survival on a study of inbreeding
in African wild dogs.

DNA and Disease

One of Fleischer’s major long-term research
programs focuses on avian malaria:
the parasite that causes the disease, the
mosquitoes that transmit it, and the birds
that suffer from it. Avian malaria is similar
to human malaria but only some birds are
susceptible; species that evolved with the
parasite have resistance to its ill-effects.
But neither the parasites nor the mosquitoes
that transmit them were found in
Hawaii until after the mosquitoes were
accidently introduced in the 1800s and
the malaria in the 1900s. For many of the
islands’ native birds, avian malaria was
lethal, and the disease contributed to the
extinction or near-extinction of a host of
birds. Hawaii’s 57 species of honeycreepers
were particularly hard hit, with avian
malaria dealing a death blow to many of
the more than 30 species that went extinct
in the last few hundred years. And avian
malaria continues to limit the distributions
of the remaining species to high-elevation
forests where colder temperatures don’t
favor the mosquitoes.

Using his DNA detective’s tool kit,
Fleischer and his colleagues have determined
that some honeycreepers are evolving
resistance to avian malaria and thus are
recovering in low-elevation forests. This
is the good news. The bad news is that a
different genetic type of the parasite-transmitting
southern house mosquito, more
recently arrived in Hawaii, may be capable
of thriving at high elevations.

In a study that looked at the DNA of
more than 700 southern house mosquitoes
from around the world, the researchers
found that there are several distinct genetic
strains of the species. The first strain to
reach Hawaii was from a New World
source—perhaps Mexico. Since then,
however, at least one other strain has been
introduced, this time from the southern
Pacific, and these mosquitoes are adapted
to cold environments like those of New
Zealand in summer—and high-elevation
habitats in Hawaii.

The long-term impacts of this genetic
discovery about mosquito adaptability are
still to be determined, but you can be sure
that Genetics Lab scientists will be on
case. As long as they keep translating the
stories told by genes, we can better understand
changes in the natural world.

—Freelance writer Susan Lumpkin has
written several articles on the fascinating work
of the Zoo’s Genetics Lab.